Contacts of the helix formed by residues 134 - 140 (chain A) in PDB entry 1EQB
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with ASN 134 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99A SER* 5.7 0.2 + - - -
127A LEU* 3.5 23.9 + - + +
128A THR* 3.5 25.2 - - - +
131A SER* 3.1 15.7 + - - +
133A VAL* 1.3 80.2 - - + +
135A PHE* 1.3 74.2 + - - +
136A SER* 2.7 34.2 + - - -
137A GLY 3.1 10.2 + - - -
138A LYS* 3.1 18.1 + - - +
258B PRO 2.9 24.1 + - - +
259B GLY 3.4 7.7 + - - -
260B GLY* 5.1 1.6 - - - -
261B GLN 5.2 3.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 135 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99A SER* 4.0 7.0 - - - -
103A PHE* 3.5 54.7 - + + -
106A TYR* 3.8 30.5 - + + -
128A THR* 4.0 19.3 - - + -
134A ASN* 1.3 95.3 + - - +
136A SER* 1.3 73.2 + - - +
138A LYS* 4.4 8.0 - - - +
139A LEU* 2.9 51.4 + - + +
140A TYR* 4.9 2.9 - + - -
103B PHE* 4.5 14.1 - + + -
107B THR* 5.9 2.5 - - + -
259B GLY* 3.0 20.2 + - - +
260B GLY* 4.2 15.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 136 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106A TYR* 3.6 14.1 - - - -
127A LEU 3.2 7.6 + - - -
128A THR* 3.5 18.8 - - - -
130A GLY* 3.0 25.8 + - - -
131A SER 3.5 0.9 + - - -
134A ASN* 2.7 22.9 + - - -
135A PHE* 1.3 87.9 - - - +
137A GLY* 1.3 59.8 + - - +
140A TYR* 3.3 35.4 + - - +
142A ILE* 3.9 4.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 137 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130A GLY 3.7 12.6 - - - -
131A SER 3.2 18.0 + - - -
132A PRO* 4.1 8.5 - - - +
134A ASN 3.1 4.0 + - - -
136A SER* 1.3 82.8 + - - +
138A LYS* 1.3 62.8 + - - +
140A TYR 3.4 11.9 - - - +
142A ILE* 4.3 6.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 138 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132A PRO 3.4 13.4 + - - +
133A VAL* 3.1 36.8 + - - +
134A ASN 3.1 13.1 + - - +
135A PHE* 3.9 6.1 - - - +
137A GLY* 1.3 79.8 - - - +
139A LEU* 1.3 67.2 + - + +
140A TYR 4.7 0.7 - - - +
107B THR* 5.7 9.0 - - - +
112B PRO* 5.5 3.1 - - - +
259B GLY* 5.1 4.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 139 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103A PHE* 4.6 10.8 - - + -
107A THR* 5.8 1.6 - - + -
112A PRO* 3.5 11.3 - - + +
113A GLY* 2.8 23.6 + - - -
135A PHE* 2.9 41.3 + - + +
138A LYS* 1.3 82.8 - - + +
140A TYR* 1.3 84.0 + - + +
103B PHE* 5.2 3.6 - - + -
107B THR* 5.8 7.2 - - + -
112B PRO* 3.9 27.8 - - + -
139B LEU* 4.5 31.2 - - + -
140B TYR* 6.1 0.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 140 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106A TYR* 3.5 53.7 + + + +
107A THR* 3.9 15.4 + - - +
110A LEU* 4.0 18.3 + - + -
111A GLU 3.5 28.0 - - - -
112A PRO* 3.8 13.7 - - + +
113A GLY* 3.8 4.9 - - - +
114A ASP 3.6 11.0 - - - +
116A VAL* 4.3 11.4 - - + -
135A PHE* 4.7 4.3 - + - -
136A SER* 3.3 23.4 + - - +
137A GLY 3.4 16.6 - - - +
138A LYS 3.5 0.7 - - - +
139A LEU* 1.3 103.5 - - + +
141A ASN* 1.3 62.6 + - - +
142A ILE* 3.5 6.6 + - + +
139B LEU* 6.1 0.7 - - - +
----------------------------------------------------------
Back to top of page
A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il